People have been evacuated using tractors and boats from neighborhoods that have been submerged in water in Beledweyne town after days of rainfall and flooding, the charity said.
Thousands of residents in makeshift camps are in desperate need of food and water, the organization said.
Save the Children said its staff are working tirelessly screening children, but resources are inadequate to address the humanitarian scale of the problem.
“Somalia is on the front line of the climate crisis, and resources are being stretched to their limits,” Mohamud Mohamed Hassan, Save the Children Somalia Country Director said.
OCHA said three people, including two children were reported to have drowned after a river in the town burst its banks on Saturday due to the rains. A boat carrying 20 people also capsized on the river, and many passengers are feared missing, the UN agency said in a report.
Floods from the river had destroyed farmlands, roads, and other infrastructure in surrounding areas, according to the UN agency.
Somali government has set up an emergency committee to coordinate humanitarian response assistance with organizations in affected areas.